To reduce mercury content in rice grains and ensure food security, this study investigated water management practices suitable for rice paddies with mild to moderate mercury contamination in the Yangtze River Delta region. The effects of different water regulation models and rice varieties on mercury uptake and accumulation in brown rice were systematically studied through field sampling, field experiments, and pot experiments. Field sampling revealed that the mercury content in brown rice of the Suxiangjing 1176 was significantly lower in the drying treatment than in the flooding treatment (P < 0.05). While no significant difference was observed for the Nanjing 3908, the mercury content in the drying treatment was still slightly lower. Field experiments demonstrated that drying treatment significantly reduced the mercury content in brown rice of the Changxiangjing 1813 by 59.38% compared to flooding treatment. Significant varietal differences were observed in the response to water management: the Ningxiangjing 9 exhibited the lowest mercury bioaccumulation factor (BAF_Hg) of 0.66 under drying treatment, whereas the Nanjing 3908 showed no significant response, consistent with the field sampling results. Plot experiments further showed that the mercury content in brown rice of the Nanjing 46 under shallow wet irrigation (HW-2, 2 cm water depth) was 16.71 μg/kg, which is 49% lower than that under conventional irrigation (HW-5) at 32.77 μg/kg, and below the national standard limit. This reduction is primarily attributed to the inhibition of mercury migration in the soil due to decreased soil moisture. In contrast, pot experiments indicated that merely altering the water layer height (3 cm, 6 cm, 9 cm) had no significant effect, thereby clarifying that "moderate water stress" rather than the absolute water volume is the key factor. Consequently, the study recommends adopting the feasible agronomic practice of "shallow wet irrigation (2 cm water depth) + low-accumulation varieties" as an effective solution for managing mercury contamination in regional paddy fields.